Submission rules for all types of groups
- Predictions in CASP15 may be submitted in 3 formats:
TS # Atomic coordinates (tertiary or quaternary structure)
QA # Model accuracy assessment
LG # Ligand
- One team may make a prediction of a target by submitting up to five models
in the TS or LG categories, and one model in the QA category.
- Submissions for regular prediction targets, assembly targets, protein-ligand
complexes, RNA structure, and data-assisted targets should be submitted in the TS format.
- Each submission file should contain prediction for only one target.
- Each submission file should contain only one of the allowed format categories.
- Submission files in QA category should contain only one model.
- Submission files in TS categories may contain either one or several
models. Most of the evaluation and assessment will focus on
the model labeled '1' (model index 1, see MODEL record). Each model should
begin with the MODEL record, end with the END record, and contain no target
residue repetitions. You may specify only one set of required header fields
(PFRMAT, TARGET, AUTHOR, METHOD) above the first MODEL record in the prediction
file. A multiple-model file will be split into separate files (one model per
file) and each model (up to 5) will be sent separately to the verification server.
- Submission of a duplicate model (same target, format category, group, model
index) will replace previously accepted model, provided it is received before
the deadline.
- Each submission must begin with the PFRMAT, TARGET and AUTHOR records,
contain the METHOD field and at least one block starting with the MODEL
and ending with the END record.
- Each submitted model is automatically verified by the format verification
server. In case of successful submission no confirmation email will be sent.
A unique model ACCESSION CODE is composed from the number of the target, prediction
format category, prediction group number, and model index.
Example:
Accession code T0444TS005_2 has the following components:
T0444 target number
TS Tertiary Structure (PFRMAT TS)
005 prediction group 5
2 model index 2
The accepted predictions could be viewed using Model Viewer link from the CASP15
web page.
If the submission contains an error, the regular group leader or server contact
person will be immediately notified through email. If your prediction is rejected
for format inconsistency, you will have the possibility to correct problems and
re-send prediction(s) within the target prediction time window.
Submission rules for expert groups (usually, 3-week deadline in TS category, 2 day deadline for QA)
-
Predictions can be submitted by a group leader or a group member with submission
privileges. The group leader can set the privileges (regular member or submitter)
for every member of his group using the 'Review member status' option from
'My CASP15 profile' link. Members of prediction groups who intend to submit predictions
should receive submission permission from the group leader first and then use
the 12-digit Registration Code of the group to submit predictions for that group.
- Models for regular deadline groups should be submitted directly by e-mail to
models AT predictioncenter.org or using
the CASP15 model submission facility.
-
When sending predictions by email, please send them in the body of the message.
-
When sending predictions by email, please remember to use only the email address
registered with the Prediction Center as origination points (make sure we have
the updated email address for you on file - check for this your "My Personal Data"
link from the menu). If you temporary cannot use the registered email address for
submission, please use the submission form
instead.
-
Time for returning regular group predictions is set separately for each target.
Usually regular deadline predictors have around 3 weeks
from the date of target release to return a prediction.
-
Predictions in TS categories should be normally sent only on all-group targets.
-
Predictions in LG category should be sent for targets where Additional Information
and Ligand fields in the target-specific Target List pages indicate availability
of ligands.
-
Predictions in TS categories should contain sensible residue confidence estimates in
the column reserved for the B-factor value in the PDB format.
-
Predictions in QA category should be sent for all multimeric targets.
-
Multichain predictions should be sent for heteromeric targets (names starting with 'H')
and homo-oligomeric targets (names starting with 'T' and stoichiometry parameter other than A1).
The stoichiometry information for each target will be provided in the column 'Stoichiom'
in the Target List page.
Submission rules for server groups (3-day deadline in TS categories, 2 day deadline for QA)
Format description
All submissions must start with a CASP header.
Records in the header must begin with a standard keyword
starting in the first column of the line.
The mandatory records should be listed in the following order:
PFRMAT Format specification code: TS , QA, LG
TARGET Target identifier from the CASP15 target table
AUTHOR XXXX-XXXX-XXXX Registration code of the Group Leader or Server Group Name
METHOD Records describing the methods used
MODEL Beginning of the data section for the submitted model
...
END End of the submitted model
Some header records are specific to prediction categories and
should follow the first five mandatory records specificed above.
PARENT TS category, mandatory. Specifies templates used to generate the model.
TER TS category, mandatory. Terminates chain in a TS model.
SCORE TS category, optional. Reliability of the model (overall fold).
QSCORE TS category, optional. Reliability of the interfaces in the quaternary structure of the model.
REMARK All categories, optional. Comment record. May appear anywhere after the first 3 required lines.)
QMODE QA category, mandatory. Specifies type of the QA prediction.
LIGAND LG category, mandatory. Ligand name (beginning of the ligand data section).
POSE LG category, mandatory. Pose number for the modeled ligand.
Models should be submitted in Plain Text format.
Record PFRMAT should appear on the first line of the prediction and
is used for all submissions.
PFRMAT TS
TS indicates that submission contains 3D atomic coordinates
in standard PDB format
PFRMAT QA
QA indicates that submission contains estimates of model accuracy
PFRMAT LG
LG indicates that the submission contains the 3D atomic coordinates
of the ligand in standard MDL format (https://en.wikipedia.org/wiki/Chemical_table_file).
Record TARGET should appear on the second line of the prediction and
is used for all submissions.
TARGET Txxxx
Txxxx indicates id of the target predicted.
Record AUTHOR should appear on the third line of the prediction
and is used for all submissions.
For all groups:
AUTHOR XXXX-XXXX-XXXX
XXXX-XXXX-XXXX indicates the Group Registration code.
This is the code obtained by the group leader upon registration.
Note: Members of prediction groups who intend to submit predictions
should receive submission permissions from the group leader and
use the registration code of the Group for all predictions submitted by
that group. If sending predictions by email, please send them from the
registered emails of the group leader or group submitter.
If you temporary can not use these emails for submission, please login
to our website and then use our web-based submission facility.
Servers alternatively can be identified using their registered group names:
AUTHOR MY_SERVER_NAME
or
REMARK AUTHOR MY_SERVER_NAME
where MY_SERVER_NAME is a name selected for the server group at registration
Records METHOD are used for all submissions.
These records describe the method used. Predictors are urged to provide
a concise description of the method, including data libraries used,
and values of default and non-default parameters.
Record MODEL is used for all submissions.
Signifies the beginning of model data.
MODEL n
n Model index n is used to indicate predictor's ranking
according to her/his belief which TS model is closest to the
target structure (1 <= n <= 5). Model index is included
automatically in the ACCESSION CODE. All models with index
higher than 5 will be discarded.
Model index should be set to 1 in QA category.
SCORE Used in TS predictions. This record specifies a model reliability score in range [0.0, 1.0] which will be evaluated in the EMA self-assessment. Reflects similarity of the full model/complex to the target upon global superposition (GDT/TM style). Independently from that value, the average per-residue scores derived from the B-factors will be evaluated against full-atomic superposition-independent scores.
QSCORE Used in assembly predictions. Optional. This record specifies a quaternary structure reliability score (interface accuracy) in range [0, 1] which is evaluated in EMA self-assessment. Will be evaluated against interface contact-based scores (e.g. DockQ, QS-score).
REMARK Optional. PDB style 'REMARK' records may be used
anywhere in the submission. These records may contain any
text and will in general not influence evaluation.
Record PARENT is required for submissions in the TS format.
PARENT record indicates structure templates used to generate the MODEL
(see description of the TS format below).
One PARENT record is required for every monomeric prediction,
every homo-multimeric model (should be placed within the first chain),
and every subunit (first chain of every different sequence) of
hetero-multimeric models.
PARENT N/A
Indicates that a prediction is not directly based on any known
structure. Note that this is the only indication in the file that the
prediction is ab initio, so is a critical piece of information.
PARENT 1abc_A
Indicates that a single PDB entry 1abc, chain A
was used as a modeling template.
All template-based predictions should be submitted with this form
of the PARENT record. Note that, in order to be accepted, the code
must correspond to a current PDB entry.
PARENT 1cdc 2def_g [3hij_k ...]
Indicates that the model is based on more than one structural template.
Up to five PDB chains may be listed here with additional detailed information
included in the METHOD records.
TER record is required in TS predictions to indicate chain termination.
TER
QMODE record is required in QA predictions to indicate type of prediction.
QMODE n
n=1 : global model quality scores (MQS - two numbers per model)
n=2 : MQS and interface reliability estimates on per-residue basis.
LIGAND record is required in LG predictions to indicate the beginning of the ligand data.
Each ligand should be submitted under a separate LIGAND record.
LIGAND n XXX
n The ligand number as provided in the SMILES file accessible
from the target-specifc Target List page.
XXX Name of the ligand as provided in the released SMILES file.
POSE record is required in LG predictions to indicate number of the predicted pose
of the ligand.
POSE n
n Pose index n is used to indicate predictor's ranking according to
her/his belief which ligand pose (conformation) is closest to that
in the target structure (1 <= n <= 5). All ligands with index higher
than 5 will be discarded.
END record is used for all predictions and indicates the end of a
single model submission.
Atomic coordinates (proteins) (PFRMAT TS).
Standard PDB atom records are used for the atomic coordinates. Format of the
submission requires that 80 column long records are used (Example 1).
These may be spaces
when needed (see target template PDB files as provided in specific target
descriptions available through the CASP15 target table).
Coordinate section for each monomeric model, each homo-oligomeric model,
or every new (different sequence) chain of hetero-multimeric model should begin
with a single PARENT record and terminate with a TER record (see above).
If a multimer's stoichiometry composition formula displays more than one equivalent
unit, the PARENT record should be supplied within the first unit only.
It is requested that coordinate data be supplied for at least all
non-hydrogen main chain atoms, i.e. the N, CA, C and O atoms of every residue.
For any given MODEL, no target residue may be repeated in the prediction.
For assembly prediction (Example 2), coordinates for all chains should be submitted
in one PDB-like file. Chains should be labeled 'A', 'B', ... according
to the provided template for each target. The convention for chain order is:
alphabetical, heteromeric units (different sequences) first. For example,
for a homotrimer of heterodimers please name chains in the following order:
AB (first hetero-dimer), CD (second dimer), EF (3rd dimer).
Names of heteromeric targets will start with letter 'H', e.g. H0960,
names of all other regular targets will start from letter 'T', e.g. T1001.
Homo-multimeric predictions are encouraged for all other regular targets,
if applicable. If subunits of heteromeric targets are additionally released
as separate tertiary structure prediction targets,
there will be no need to submit monomeric predictions in addition to multimeric:
we will automatically extract coordinates of each first different chain from
the assembly prediction and save it as a tertiary structure model for the
corresponding subunit.
Information on the tentative oligomeric state of the protein (the stoichiometry formula
to the best of our knowledge at the time of target release), will be announced through
the Target List page.
If a prediction is for protein-RNA complex, protein chains should be named alphabetically
and RNA chains numerically.
Atoms for which a prediction has been made must contain a value between 0.01 and 1.00
(usually "1.00") in the occupancy field; those for which no prediction has been
made must either contain "0.00" in that field or be skipped altogether.
In place of temperature factor field, percentage-scale confidence estimates (0-100) should be
provided (100.00 for highly confident prediction). The estimates should assess accuracy
of the relative positions of atoms in the neighborhood (incl. other chains in the
case of complexes). Evaluation will be based on full-atomic superposition-independent
scores (e.g. lDDT, CAD) on the level of residues, i.e. a residue confidence estimate
is derived from averaging the confidence values of all its atoms.
Models with all residues having the same 'B-factor' will be rejected.
Atomic coordinates (RNA) (PFRMAT TS, target name starting from 'R' for RNA structures and 'A' for protein-RNA complexes).
A CASP RNA submission may contain up to five RNA 3D models in the
RNA-Puzzles community standard pretexted by the CASP keywords
(see Format Description section above, and Example 3).
Coordinates should be provided for all nucleotides provided in the target FASTA file.
Only standard nucleotides (A, C, U, and G) should be used. Modified nucleotides
will be treated as unmodified ones. All additional atoms will be discarded.
Only the following atoms will be considered:
(1) for nucleobases: C2, C4, C6, C8, N1, N2, N3, N4, N6, N7, N9, O2, O4, and O6
(2) for sugar-phosphate backbones: C1', C2', C3', C4', C5', O2', O3', O4', O5', OP1, OP2, and P
[1].
CASP will provide RNA sequence (in the FASTA format) of the target
through the target-specific web page from the Target List page.
FASTA header will contain target ID (e.g., T1001) and chain ID (number from 0 to 9)
for every different strand in the structure. Body of the FASTA file will contain
nucleic acid sequence, e.g.
> T1001 0
GGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUUC
CASP will provide a 3D structure template for the target
through the target-specific web page from the Target List page.
We will generate a PDB template for each RNA target using the
rna_puzzles_format.py script from package [2]:
python rna_puzzles_format.py [FASTA file] > [Template.pdb]
All predictions should comply with the provided PDB template.
To ensure correctness of your RNA 3D prediction [2], you can run
python format_check.py [Prediction.pdb] [Template.pdb] .
The script verifies: (1) the expected number of residues and atoms
included in the particular prediction (all hydrogens must be discarded)
and (2) ordering of residues and atoms with respect to the template.
If a prediction is in correct format (i.e., it contains all required
nucleotides and their atoms in the requested order),
the script will finish with a success message,
otherwise an error message will be generated and written to
'xx.format_check.txt' file.
If you have a complete 3D prediction and want to bring it to the
RNA-Puzzles community standard, you can use the rna-tools package [3]
provided within the RNA-Puzzles toolkit [4]. Please run:
rna_pdb_toolsx.py --get-rnapuzzle-ready *pdb --inplace
For protein-RNA complexes, protein chains should be named alphabetically (A,B,C,...)
while RNA strands numerically (0,1,2,...) - see Example 4.
References:
[1] Cruz, J. A., Blanchet, M. F., Boniecki, M., Bujnicki, J. M., Chen, S.
J., Cao, S., ... & Westhof, E. (2012). RNA-Puzzles: a CASP-like evaluation
of RNA three-dimensional structure prediction. Rna, 18(4), 610-625.
[2] https://github.com/chichaumiau/RNA-Puzzzles_format
[3] https://github.com/mmagnus/rna-tools
[4] Magnus, M., Antczak, M., Zok, T., Wiedemann, J., Lukasiak, P., Cao,
Y., ... & Miao, Z. (2020). RNA-Puzzles toolkit: a computational resource
of RNA 3D structure benchmark datasets, structure manipulation, and
evaluation tools. Nucleic acids research, 48(2), 576-588.
Estimation of model accuracy (PFRMAT QA).
In QA category, predictors are requested to use model index '1' for predictions.
Data are inserted between MODEL and END records of the submission file.
You may submit your quality assessment prediction in one of the two different modes:
QMODE 1 : global model quality scores (MQS - two numbers per model)
QMODE 2 : MQS and interface reliability estimates on per-residue basis.
The first line of data should specify mode identifier, i.e. QMODE (see Example 5).
QMODE1 (Example 5A):
The first column in each line contains model identifier (file name of the accepted
3D prediction). The second and third columns contain two accuracy scores for a model.
The accuracy scores are real numbers in range [0.0, 1.0] (1.0 being a perfect model)
predicting overall fold accuracy (i.e. a score conceptually similar to the self-estimated
SCORE value in the TS format, see above) and overall interface accuracy (a score
conceptually similar to the self-estimated QSCORE value in the TS format).
If you do not provide the interface accuracy estimate (second MQS number), please
put 'X' in place of the score.
QMODE2 (Example 5B):
If you additionally provide estimates of residues being in the interface,
you should provide confidence scores in range [0.0,1.0] for all interface
residues observed in the model. These should be provided additionally to the
information provided in QMODE1 (see Example 5B). Interface residues are defined
as having a contact with at least one residue from another chain (CB-CB distance <=8A,
CA in case of Glycine). The confidence relates to the probability of an atom
being in the actual interface of the native structure in the format
[chain_name][res_num]:[confidence_score] (e.g. A26:0.90).
Note.
Please, be advised that a QA record line n QMODE2 may be too long to fit all interface residues,
and that some editors/mailing programs may force line wrap potentially causing unexpected
parsing errors. To avoid this problem we recommend that you split long lines into
shorter sublines (50-100 columns of data) by yourself. Our parser will consider
consecutive sublines (starting with the line containing evaluated model name and
ending with the line containing the next model name or tag END) a part of the same
logical line.
Prediction of ligand poses (PFRMAT LG).
Targets for Ligand prediction can be of two types:
(1) regular tertiary structure or assembly targets containing ligands
(target names starting with T or H, e.g. T1999), and
(2) targets intended exclusively for ligand prediction
(names starting with L, e.g. L2999).
[Update. The ligand-only targets will start
with T or H, but will be marked as Ligand and Server-only at the same time.]
The same model submission procedure applies to both.
Information on the known ligands in the targets will be communicated
to predictors through the Additional Information field in the
target-specific Target List pages, and also
provided as a text file (e.g., T1999.smiles.txt).
Each ligand prediction, e.g. T1999LG000_3, must be accompanied by the structure
prediction T1999TS000_3 of the corresponding protein receptor in the same frame
of reference. The receptor prediction should be submitted separately as a regular
TS prediction. MODEL records in the linked TS and LG predictions should coincide.
Prediction of atomic coordinates of ligand poses should be included only
in the LG-format submissions, and not in the TS ones.
LG models without the corresponding TS models will be ignored.
Each LIGAND record, e.g.
LIGAND 001 LIG
starts a data block specific to the ligand ID (see Example 6).
The ligand number in this record indicates that the subsequent data block
is for the ligand '001' from the SMILES file, e.g.:
001 LIG CC(C)N1CCN(CC1)C(=O)C2=CC=CS2
002 LIG CC(C)N1CCN(CC1)C(=O)C2=CC=CS2
003 MG [Mg+2]
Note that in this case there are two instances of the same ligand LIG (001 and 002)
in the SMILES file, and each of the instances should be submitted under a separate
LIGAND record.
Each ligand can be modeled in up to 5 poses. Poses should be submitted under
the same LIGAND record and have to be ordered by their expected accuracy.
Each pose starts with the keyword 'POSE' followed by the pose number.
Blocks of information for each POSE should contain data in the MDL format (described below).
Predictors should ensure that atoms are properly connected by bonds in the Bonds block,
according to the definition of the ligand given by the canonical SMILES string.
Submissions with incorrect connectivity will be marked as invalid.
Hydrogen atoms are optional and can be omitted.
MDL Format description
All submitted ligand models files should be submitted in MDL format and must include the following information:
- Header block
- Counts line
- Atom block
- Bonds block
- End line
- Model delineation line
Templates for submitting ligands can be generated with the template_gen.py script (Usage: python template_gen.py ) N.b the script uses RDKit to canonicalise SMILES strings and generate output. Instructions for installing RDKit can be found here:
https://www.rdkit.org/docs/Install.html
Header block
Consists of three lines.
The first is the title line, which can be blank but must exist.
The second line is the Program/ time stamp line
(The name of the program used for structure generation).
The third is a blank line.
Counts line
The counts line is a series of 11 entries e.g.
17 18 0 0 0 0 0 0 0 0999 V2000
The first two numbers are required and denote the number of
atoms and bonds in the file respectively.
Atom block
There should be a single entry on each line for every atom in the structure.
The first three entries are 10 characters each and specify
the atom coordinates in the x, y , and z dimensions, respectively.
Atom coordinates are followed by a space and the chemical symbol of the atom.
The chemical symbol is followed by a number of entries relating to chemical
properties. These may be left as zeros.
Bonds block
There should be a single entry on each line for every bond in the structure.
The important numbers are the first number that represents the first atom number
in the bond, the second number representing the second atom in the bond,
and the third number representing the bond type.
Bond types are denoted as follows:
1= Single, 2 = Double, 3 = Triple, 4 = Aromatic,
5 = Single or Double, 6 = Single or Aromatic, 7 = Double or Aromatic, 8 = Any.
End line
The bonds block must be immediately followed by a line denoting
the end of the model as such:
M END
Example 1. Atomic coordinates (Tertiary Structure)
The primary CASP15 format used for tertiary structure prediction
An example of a monomeric prediction.
PFRMAT TS
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT 1abc 1def_A
ATOM 1 N GLU 1 10.982 -9.774 1.377 1.00 90.00
ATOM 2 CA GLU 1 9.623 -9.833 1.984 1.00 85.50
ATOM 3 C GLU 1 8.913 -11.104 1.521 1.00 85.50
ATOM 4 O GLU 1 9.187 -11.630 0.461 1.00 80.00
ATOM 5 CB GLU 1 8.814 -8.614 1.546 1.00 85.45
ATOM 6 CG GLU 1 7.372 -8.754 2.039 1.00 75.00
ATOM 7 CD GLU 1 7.339 -8.625 3.562 1.00 93.50
ATOM 8 OE1 GLU 1 8.370 -8.307 4.131 1.00 90.50
ATOM 9 OE2 GLU 1 6.284 -8.846 4.132 1.00 85.40
ATOM 10 N THR 2 7.998 -11.599 2.304 1.00 70.60
ATOM 11 CA THR 2 7.266 -12.832 1.907 1.00 75.60
ATOM 12 C THR 2 6.096 -12.456 1.005 1.00 76.40
ATOM 13 O THR 2 5.008 -12.217 1.466 1.00 75.60
ATOM 14 CB THR 2 6.731 -13.533 3.157 1.00 70.90
ATOM 15 OG1 THR 2 7.662 -13.379 4.220 1.00 80.60
ATOM 16 CG2 THR 2 6.526 -15.019 2.864 1.00 83.46
ATOM 17 N VAL 3 6.308 -12.396 -0.278 1.00 50.70
ATOM 18 CA VAL 3 5.190 -12.030 -1.187 1.00 45.60
ATOM 19 C VAL 3 3.954 -12.870 -0.844 1.00 59.70
ATOM 20 O VAL 3 2.834 -12.471 -1.090 1.00 47.30
ATOM 21 CB VAL 3 5.608 -12.274 -2.641 1.00 44.00
ATOM 22 CG1 VAL 3 5.542 -13.771 -2.959 1.00 30.70
ATOM 23 CG2 VAL 3 4.664 -11.514 -3.573 1.00 40.35
ATOM 24 N GLU 4 4.146 -14.029 -0.272 1.00 80.70
ATOM 25 CA GLU 4 2.976 -14.882 0.086 1.00 83.60
ATOM 26 C GLU 4 2.153 -14.190 1.175 1.00 80.50
ATOM 27 O GLU 4 0.942 -14.141 1.109 1.00 85.40
ATOM 28 CB GLU 4 3.465 -16.238 0.597 1.00 87.55
ATOM 29 CG GLU 4 2.336 -17.264 0.479 1.00 81.20
ATOM 30 CD GLU 4 2.929 -18.671 0.391 1.00 70.10
ATOM 31 OE1 GLU 4 4.056 -18.846 0.823 1.00 77.75
ATOM 32 OE2 GLU 4 2.246 -19.551 -0.108 1.00 80.90
TER
END
Example 2. Assembly prediction (quaternary structure)
An example of prediction for a homodimer of heterodimers.
PFRMAT TS
TARGET H0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT N/A
ATOM 1 N ALA A 2 66.410 61.318 7.312 1.00 80.56 N
ATOM 2 CA ALA A 2 67.149 60.105 6.984 1.00 80.55 C
ATOM 3 C ALA A 2 66.481 58.861 7.568 1.00 80.24 C
ATOM 4 O ALA A 2 66.323 57.855 6.871 1.00 80.19 O
ATOM 5 CB ALA A 2 68.602 60.207 7.448 1.00 80.18 C
ATOM 6 N ARG A 3 66.088 58.921 8.836 1.00 50.80 N
ATOM 7 CA ARG A 3 65.379 57.793 9.441 1.00 50.96 C
ATOM 8 C ARG A 3 63.851 57.931 9.360 1.00 50.56 C
ATOM 9 O ARG A 3 63.225 58.629 10.165 1.00 50.84 O
ATOM 10 CB ARG A 3 65.832 57.564 10.878 1.00 50.52 C
ATOM 11 CG ARG A 3 67.276 57.122 11.014 1.00 50.18 C
ATOM 12 CD ARG A 3 67.694 57.037 12.485 1.00 50.62 C
ATOM 13 NE ARG A 3 67.073 55.906 13.171 1.00 50.65 N
ATOM 14 CZ ARG A 3 67.192 55.663 14.473 1.00 50.45 C
ATOM 15 NH1 ARG A 3 67.898 56.480 15.241 1.00 50.61 N
ATOM 16 NH2 ARG A 3 66.596 54.608 15.011 1.00 50.01 N
ATOM 17 N ILE A 4 63.261 57.272 8.370 1.00 80.59 N
ATOM 18 CA ILE A 4 61.810 57.250 8.216 1.00 80.32 C
ATOM 19 C ILE A 4 61.262 56.084 9.014 1.00 80.36 C
ATOM 20 O ILE A 4 61.515 54.920 8.685 1.00 80.81 O
ATOM 21 CB ILE A 4 61.418 57.061 6.750 1.00 80.05 C
ATOM 22 CG1 ILE A 4 61.958 58.216 5.903 1.00 80.45 C
ATOM 23 CG2 ILE A 4 59.899 56.935 6.606 1.00 80.20 C
ATOM 24 CD1 ILE A 4 61.682 58.059 4.405 1.00 80.87 C
TER
PARENT 1abc
ATOM 577 N GLN B 1 28.350 17.252 8.838 1.00 70.30 N
ATOM 578 CA GLN B 1 28.340 18.142 7.644 1.00 70.24 C
ATOM 579 C GLN B 1 28.765 19.556 8.023 1.00 70.61 C
ATOM 580 O GLN B 1 28.866 19.893 9.209 1.00 70.62 O
ATOM 581 CB GLN B 1 26.941 18.176 7.013 1.00 70.82 C
ATOM 582 CG GLN B 1 26.851 19.045 5.768 1.00 70.64 C
ATOM 583 CD GLN B 1 26.103 18.370 4.654 1.00 70.30 C
ATOM 584 OE1 GLN B 1 26.147 17.151 4.527 1.00 70.37 O
ATOM 585 NE2 GLN B 1 25.426 19.152 3.825 1.00 70.67 N
ATOM 586 N LYS B 2 29.007 20.382 7.007 1.00 50.53 N
ATOM 587 CA LYS B 2 29.423 21.760 7.223 1.00 50.08 C
ATOM 588 C LYS B 2 28.253 22.741 7.066 1.00 50.20 C
ATOM 589 O LYS B 2 27.489 22.695 6.100 1.00 50.51 O
ATOM 590 CB LYS B 2 30.561 22.104 6.264 1.00 50.06 C
ATOM 591 CG LYS B 2 31.277 23.381 6.592 1.00 50.24 C
ATOM 592 CD LYS B 2 32.723 23.323 6.153 1.00 50.30 C
ATOM 593 CE LYS B 2 33.560 22.551 7.144 1.00 50.91 C
ATOM 594 NZ LYS B 2 34.976 23.004 7.075 1.00 50.63 N
ATOM 595 N THR B 3 28.120 23.623 8.047 1.00 70.04 N
ATOM 596 CA THR B 3 27.054 24.606 8.062 1.00 70.76 C
ATOM 597 C THR B 3 27.306 25.741 7.072 1.00 70.84 C
ATOM 598 O THR B 3 28.422 25.912 6.574 1.00 70.53 O
ATOM 599 CB THR B 3 26.897 25.215 9.469 1.00 70.71 C
ATOM 600 OG1 THR B 3 28.028 26.045 9.770 1.00 70.75 O
ATOM 601 CG2 THR B 3 26.807 24.118 10.507 1.00 70.32 C
TER
ATOM 70 N ALA C 2 17.139 38.489 7.542 1.00 80.40 N
ATOM 71 CA ALA C 2 16.401 39.708 7.233 1.00 80.49 C
ATOM 72 C ALA C 2 17.081 40.939 7.824 1.00 80.51 C
ATOM 73 O ALA C 2 17.221 41.955 7.138 1.00 80.84 O
ATOM 74 CB ALA C 2 14.954 39.610 7.712 1.00 80.41 C
ATOM 75 N ARG C 3 17.504 40.862 9.087 1.00 40.11 N
ATOM 76 CA ARG C 3 18.215 41.993 9.686 1.00 40.09 C
ATOM 77 C ARG C 3 19.746 41.845 9.588 1.00 40.10 C
ATOM 78 O ARG C 3 20.379 41.144 10.389 1.00 40.06 O
ATOM 79 CB ARG C 3 17.779 42.223 11.128 1.00 40.49 C
ATOM 80 CG ARG C 3 16.326 42.657 11.272 1.00 40.72 C
ATOM 81 CD ARG C 3 15.905 42.771 12.734 1.00 40.86 C
ATOM 82 NE ARG C 3 16.538 43.899 13.407 1.00 40.46 N
ATOM 83 CZ ARG C 3 16.460 44.127 14.712 1.00 40.48 C
ATOM 84 NH1 ARG C 3 15.783 43.294 15.485 1.00 40.75 N
ATOM 85 NH2 ARG C 3 17.057 45.186 15.239 1.00 40.68 N
ATOM 86 N ILE C 4 20.329 42.493 8.586 1.00 80.62 N
ATOM 87 CA ILE C 4 21.772 42.515 8.415 1.00 80.68 C
ATOM 88 C ILE C 4 22.324 43.671 9.214 1.00 80.12 C
ATOM 89 O ILE C 4 22.056 44.830 8.893 1.00 80.89 O
ATOM 90 CB ILE C 4 22.151 42.705 6.945 1.00 80.69 C
ATOM 91 CG1 ILE C 4 21.583 41.559 6.110 1.00 80.63 C
ATOM 92 CG2 ILE C 4 23.672 42.799 6.774 1.00 80.94 C
ATOM 93 CD1 ILE C 4 21.832 41.708 4.619 1.00 80.50 C
TER
ATOM 2076 N GLN D 1 -5.202 -31.148 19.518 1.00 60.90 N
ATOM 2077 CA GLN D 1 -4.657 -29.990 20.288 1.00 60.01 C
ATOM 2078 C GLN D 1 -3.890 -30.442 21.508 1.00 60.88 C
ATOM 2079 O GLN D 1 -3.784 -29.715 22.500 1.00 60.19 O
ATOM 2080 CB GLN D 1 -5.777 -29.086 20.761 1.00 60.28 C
ATOM 2081 CG GLN D 1 -5.605 -27.661 20.342 1.00 60.13 C
ATOM 2082 CD GLN D 1 -6.792 -27.230 19.563 1.00 60.49 C
ATOM 2083 OE1 GLN D 1 -7.914 -27.444 20.008 1.00 60.58 O
ATOM 2084 NE2 GLN D 1 -6.574 -26.639 18.389 1.00 60.22 N
ATOM 2085 N LYS D 2 -3.368 -31.653 21.440 1.00 30.19 N
ATOM 2086 CA LYS D 2 -2.612 -32.197 22.545 1.00 30.61 C
ATOM 2087 C LYS D 2 -1.686 -33.248 21.993 1.00 30.53 C
ATOM 2088 O LYS D 2 -2.009 -33.946 21.031 1.00 30.89 O
ATOM 2089 CB LYS D 2 -3.545 -32.831 23.588 1.00 30.00 C
ATOM 2090 CG LYS D 2 -4.381 -31.846 24.404 1.00 30.19 C
ATOM 2091 CD LYS D 2 -5.747 -32.442 24.727 1.00 30.42 C
ATOM 2092 CE LYS D 2 -6.619 -31.499 25.543 1.00 30.82 C
ATOM 2093 NZ LYS D 2 -6.281 -31.538 26.993 1.00 30.55 N
ATOM 2094 N THR D 3 -0.512 -33.331 22.592 1.00 60.45 N
ATOM 2095 CA THR D 3 0.451 -34.328 22.187 1.00 60.41 C
ATOM 2096 C THR D 3 -0.247 -35.666 22.381 1.00 60.63 C
ATOM 2097 O THR D 3 -1.086 -35.814 23.270 1.00 60.24 O
ATOM 2098 CB THR D 3 1.689 -34.276 23.070 1.00 60.49 C
ATOM 2099 OG1 THR D 3 2.475 -33.141 22.697 1.00 60.74 O
ATOM 2100 CG2 THR D 3 2.505 -35.558 22.932 1.00 60.93 C
TER
END
Example 3. RNA structure
PFRMAT TS
TARGET R0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT N/A
ATOM 845 OP1 G 0 1 -7.077 -0.231 -13.826 1.00 70.00 O
ATOM 846 OP2 G 0 1 -4.765 -1.076 -13.098 1.00 70.00 O
ATOM 847 O5' G 0 1 -5.886 -1.981 -15.135 1.00 70.00 O
ATOM 848 C5' G 0 1 -6.709 -1.918 -16.298 1.00 70.00 C
ATOM 849 C4' G 0 1 -6.322 -3.006 -17.271 1.00 70.00 C
ATOM 850 O4' G 0 1 -4.936 -2.810 -17.669 1.00 70.00 O
ATOM 851 C3' G 0 1 -6.371 -4.421 -16.711 1.00 70.00 C
ATOM 852 O3' G 0 1 -7.670 -4.989 -16.845 1.00 70.00 O
ATOM 853 C2' G 0 1 -5.326 -5.146 -17.550 1.00 70.00 C
ATOM 854 O2' G 0 1 -5.835 -5.471 -18.831 1.00 70.00 O
ATOM 855 C1' G 0 1 -4.266 -4.057 -17.703 1.00 70.00 C
ATOM 856 N9 G 0 1 -3.258 -4.064 -16.647 1.00 70.00 N
ATOM 857 C8 G 0 1 -3.367 -3.513 -15.394 1.00 70.00 C
ATOM 858 N7 G 0 1 -2.300 -3.679 -14.662 1.00 70.00 N
ATOM 859 C5 G 0 1 -1.430 -4.385 -15.483 1.00 70.00 C
ATOM 860 C6 G 0 1 -0.113 -4.857 -15.240 1.00 70.00 C
ATOM 861 O6 G 0 1 0.571 -4.743 -14.217 1.00 70.00 O
ATOM 862 N1 G 0 1 0.402 -5.524 -16.345 1.00 70.00 N
ATOM 863 C2 G 0 1 -0.260 -5.714 -17.530 1.00 70.00 C
ATOM 864 N2 G 0 1 0.405 -6.385 -18.475 1.00 70.00 N
ATOM 865 N3 G 0 1 -1.484 -5.281 -17.772 1.00 70.00 N
ATOM 866 C4 G 0 1 -2.006 -4.630 -16.712 1.00 70.00 C
ATOM 867 P U 0 2 -8.176 -6.087 -15.783 1.00 80.00 P
ATOM 868 OP1 U 0 2 -7.261 -7.253 -15.890 1.00 80.00 O
ATOM 869 OP2 U 0 2 -9.636 -6.279 -15.978 1.00 80.00 O
ATOM 870 O5' U 0 2 -7.936 -5.396 -14.366 1.00 80.00 O
ATOM 871 C5' U 0 2 -8.944 -5.423 -13.354 1.00 80.00 C
ATOM 872 C4' U 0 2 -8.313 -5.364 -11.981 1.00 80.00 C
ATOM 873 O4' U 0 2 -7.113 -6.190 -11.983 1.00 80.00 O
ATOM 874 C3' U 0 2 -7.861 -3.976 -11.530 1.00 80.00 C
ATOM 875 O3' U 0 2 -8.105 -3.794 -10.136 1.00 80.00 O
ATOM 876 C2' U 0 2 -6.374 -3.969 -11.873 1.00 80.00 C
ATOM 877 O2' U 0 2 -5.641 -3.123 -11.006 1.00 80.00 O
ATOM 878 C1' U 0 2 -6.006 -5.417 -11.571 1.00 80.00 C
ATOM 879 N1 U 0 2 -4.810 -5.906 -12.273 1.00 80.00 N
ATOM 880 C2 U 0 2 -3.697 -6.214 -11.512 1.00 80.00 C
ATOM 881 O2 U 0 2 -3.667 -6.091 -10.301 1.00 80.00 O
ATOM 882 N3 U 0 2 -2.618 -6.672 -12.223 1.00 80.00 N
ATOM 883 C4 U 0 2 -2.537 -6.850 -13.584 1.00 80.00 C
ATOM 884 O4 U 0 2 -1.495 -7.280 -14.077 1.00 80.00 O
ATOM 885 C5 U 0 2 -3.725 -6.506 -14.300 1.00 80.00 C
ATOM 886 C6 U 0 2 -4.798 -6.057 -13.640 1.00 80.00 C
ATOM 887 P G 0 3 -8.106 -2.312 -9.507 1.00 70.00 P
ATOM 888 OP1 G 0 3 -7.806 -1.347 -10.597 1.00 70.00 O
ATOM 889 OP2 G 0 3 -7.257 -2.327 -8.289 1.00 70.00 O
ATOM 890 O5' G 0 3 -9.617 -2.089 -9.050 1.00 70.00 O
ATOM 891 C5' G 0 3 -10.568 -1.481 -9.923 1.00 70.00 C
ATOM 892 C4' G 0 3 -11.972 -1.717 -9.415 1.00 70.00 C
ATOM 893 O4' G 0 3 -12.150 -3.138 -9.157 1.00 70.00 O
ATOM 894 C3' G 0 3 -12.316 -1.039 -8.095 1.00 70.00 C
ATOM 895 O3' G 0 3 -12.776 0.296 -8.297 1.00 70.00 O
ATOM 896 C2' G 0 3 -13.400 -1.949 -7.532 1.00 70.00 C
ATOM 897 O2' G 0 3 -14.642 -1.718 -8.170 1.00 70.00 O
ATOM 898 C1' G 0 3 -12.878 -3.321 -7.955 1.00 70.00 C
ATOM 899 N9 G 0 3 -11.995 -3.946 -6.974 1.00 70.00 N
ATOM 900 C8 G 0 3 -10.630 -4.076 -7.053 1.00 70.00 C
ATOM 901 N7 G 0 3 -10.109 -4.683 -6.022 1.00 70.00 N
ATOM 902 C5 G 0 3 -11.198 -4.973 -5.210 1.00 70.00 C
ATOM 903 C6 G 0 3 -11.260 -5.628 -3.952 1.00 70.00 C
ATOM 904 O6 G 0 3 -10.334 -6.100 -3.279 1.00 70.00 O
ATOM 905 N1 G 0 3 -12.565 -5.710 -3.483 1.00 70.00 N
ATOM 906 C2 G 0 3 -13.669 -5.226 -4.136 1.00 70.00 C
ATOM 907 N2 G 0 3 -14.840 -5.400 -3.517 1.00 70.00 N
ATOM 908 N3 G 0 3 -13.629 -4.616 -5.307 1.00 70.00 N
ATOM 909 C4 G 0 3 -12.370 -4.524 -5.784 1.00 70.00 C
TER
ATOM 910 P G 1 1 -12.645 1.375 -7.111 1.00 80.00 P
ATOM 911 OP1 G 1 1 -13.262 2.636 -7.597 1.00 80.00 O
ATOM 912 OP2 G 1 1 -11.239 1.385 -6.633 1.00 80.00 O
ATOM 913 O5' G 1 1 -13.567 0.790 -5.950 1.00 80.00 O
ATOM 914 C5' G 1 1 -14.989 0.808 -6.064 1.00 80.00 C
ATOM 915 C4' G 1 1 -15.620 0.149 -4.860 1.00 80.00 C
ATOM 916 O4' G 1 1 -15.122 -1.208 -4.730 1.00 80.00 O
ATOM 917 C3' G 1 1 -15.289 0.769 -3.511 1.00 80.00 C
ATOM 918 O3' G 1 1 -16.074 1.930 -3.251 1.00 80.00 O
ATOM 919 C2' G 1 1 -15.600 -0.373 -2.550 1.00 80.00 C
ATOM 920 O2' G 1 1 -16.993 -0.482 -2.322 1.00 80.00 O
ATOM 921 C1' G 1 1 -15.141 -1.586 -3.364 1.00 80.00 C
ATOM 922 N9 G 1 1 -13.811 -2.059 -2.992 1.00 80.00 N
ATOM 923 C8 G 1 1 -12.657 -1.974 -3.733 1.00 80.00 C
ATOM 924 N7 G 1 1 -11.620 -2.488 -3.131 1.00 80.00 N
ATOM 925 C5 G 1 1 -12.119 -2.941 -1.917 1.00 80.00 C
ATOM 926 C6 G 1 1 -11.466 -3.591 -0.836 1.00 80.00 C
ATOM 927 O6 G 1 1 -10.276 -3.911 -0.731 1.00 80.00 O
ATOM 928 N1 G 1 1 -12.350 -3.872 0.199 1.00 80.00 N
ATOM 929 C2 G 1 1 -13.687 -3.569 0.199 1.00 80.00 C
ATOM 930 N2 G 1 1 -14.370 -3.919 1.290 1.00 80.00 N
ATOM 931 N3 G 1 1 -14.308 -2.966 -0.798 1.00 80.00 N
ATOM 932 C4 G 1 1 -13.470 -2.682 -1.816 1.00 80.00 C
ATOM 933 P A 1 2 -15.537 3.045 -2.223 1.00 50.50 P
ATOM 934 OP1 A 1 2 -16.462 4.203 -2.309 1.00 50.50 O
ATOM 935 OP2 A 1 2 -14.085 3.247 -2.464 1.00 50.50 O
ATOM 936 O5' A 1 2 -15.716 2.369 -0.791 1.00 50.50 O
ATOM 937 C5' A 1 2 -17.013 2.151 -0.238 1.00 50.50 C
ATOM 938 C4' A 1 2 -16.904 1.791 1.226 1.00 50.50 C
ATOM 939 O4' A 1 2 -16.439 0.417 1.339 1.00 50.50 O
ATOM 940 C3' A 1 2 -15.898 2.603 2.032 1.00 50.50 C
ATOM 941 O3' A 1 2 -16.464 3.816 2.521 1.00 50.50 O
ATOM 942 C2' A 1 2 -15.526 1.640 3.151 1.00 50.50 C
ATOM 943 O2' A 1 2 -16.539 1.573 4.137 1.00 50.50 O
ATOM 944 C1' A 1 2 -15.494 0.317 2.390 1.00 50.50 C
ATOM 945 N9 A 1 2 -14.187 0.012 1.809 1.00 50.50 N
ATOM 946 C8 A 1 2 -13.738 0.315 0.547 1.00 50.50 C
ATOM 947 N7 A 1 2 -12.511 -0.083 0.314 1.00 50.50 N
ATOM 948 C5 A 1 2 -12.125 -0.688 1.503 1.00 50.50 C
ATOM 949 C6 A 1 2 -10.931 -1.310 1.904 1.00 50.50 C
ATOM 950 N6 A 1 2 -9.860 -1.433 1.120 1.00 50.50 N
ATOM 951 N1 A 1 2 -10.874 -1.809 3.157 1.00 50.50 N
ATOM 952 C2 A 1 2 -11.949 -1.687 3.946 1.00 50.50 C
ATOM 953 N3 A 1 2 -13.126 -1.124 3.684 1.00 50.50 N
ATOM 954 C4 A 1 2 -13.149 -0.638 2.431 1.00 50.50 C
ATOM 955 P G 1 3 -15.512 5.081 2.810 1.00 80.00 P
ATOM 956 OP1 G 1 3 -16.374 6.170 3.338 1.00 80.00 O
ATOM 957 OP2 G 1 3 -14.679 5.325 1.604 1.00 80.00 O
ATOM 958 O5' G 1 3 -14.555 4.587 3.986 1.00 80.00 O
ATOM 959 C5' G 1 3 -14.929 4.745 5.355 1.00 80.00 C
ATOM 960 C4' G 1 3 -14.303 3.658 6.201 1.00 80.00 C
ATOM 961 O4' G 1 3 -13.959 2.527 5.358 1.00 80.00 O
ATOM 962 C3' G 1 3 -12.989 4.024 6.874 1.00 80.00 C
ATOM 963 O3' G 1 3 -13.208 4.736 8.089 1.00 80.00 O
ATOM 964 C2' G 1 3 -12.344 2.661 7.108 1.00 80.00 C
ATOM 965 O2' G 1 3 -12.878 2.038 8.262 1.00 80.00 O
ATOM 966 C1' G 1 3 -12.808 1.883 5.874 1.00 80.00 C
ATOM 967 N9 G 1 3 -11.806 1.812 4.814 1.00 80.00 N
ATOM 968 C8 G 1 3 -11.929 2.263 3.522 1.00 80.00 C
ATOM 969 N7 G 1 3 -10.863 2.053 2.800 1.00 80.00 N
ATOM 970 C5 G 1 3 -9.979 1.427 3.668 1.00 80.00 C
ATOM 971 C6 G 1 3 -8.656 0.958 3.456 1.00 80.00 C
ATOM 972 O6 G 1 3 -7.979 1.001 2.423 1.00 80.00 O
ATOM 973 N1 G 1 3 -8.124 0.390 4.608 1.00 80.00 N
ATOM 974 C2 G 1 3 -8.777 0.285 5.808 1.00 80.00 C
ATOM 975 N2 G 1 3 -8.095 -0.293 6.800 1.00 80.00 N
ATOM 976 N3 G 1 3 -10.008 0.716 6.022 1.00 80.00 N
ATOM 977 C4 G 1 3 -10.545 1.272 4.916 1.00 80.00 C
TER
END
Example 4. Protein-RNA complex
PFRMAT TS
TARGET A0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT N/A
ATOM 577 N GLN A 1 28.350 17.252 8.838 1.00 38.30 N
ATOM 578 CA GLN A 1 28.340 18.142 7.644 1.00 36.24 C
ATOM 579 C GLN A 1 28.765 19.556 8.023 1.00 35.61 C
ATOM 580 O GLN A 1 28.866 19.893 9.209 1.00 36.62 O
ATOM 581 CB GLN A 1 26.941 18.176 7.013 1.00 36.82 C
ATOM 582 CG GLN A 1 26.851 19.045 5.768 1.00 36.64 C
ATOM 583 CD GLN A 1 26.103 18.370 4.654 1.00 38.30 C
ATOM 584 OE1 GLN A 1 26.147 17.151 4.527 1.00 31.37 O
ATOM 585 NE2 GLN A 1 25.426 19.152 3.825 1.00 38.67 N
ATOM 586 N LYS A 2 29.007 20.382 7.007 1.00 33.53 N
ATOM 587 CA LYS A 2 29.423 21.760 7.223 1.00 30.08 C
ATOM 588 C LYS A 2 28.253 22.741 7.066 1.00 37.20 C
ATOM 589 O LYS A 2 27.489 22.695 6.100 1.00 36.51 O
ATOM 590 CB LYS A 2 30.561 22.104 6.264 1.00 33.06 C
ATOM 591 CG LYS A 2 31.277 23.381 6.592 1.00 34.24 C
ATOM 592 CD LYS A 2 32.723 23.323 6.153 1.00 37.30 C
ATOM 593 CE LYS A 2 33.560 22.551 7.144 1.00 38.91 C
ATOM 594 NZ LYS A 2 34.976 23.004 7.075 1.00 30.63 N
ATOM 595 N THR A 3 28.120 23.623 8.047 1.00 33.04 N
ATOM 596 CA THR A 3 27.054 24.606 8.062 1.00 30.76 C
ATOM 597 C THR A 3 27.306 25.741 7.072 1.00 38.84 C
ATOM 598 O THR A 3 28.422 25.912 6.574 1.00 38.53 O
ATOM 599 CB THR A 3 26.897 25.215 9.469 1.00 31.71 C
ATOM 600 OG1 THR A 3 28.028 26.045 9.770 1.00 32.75 O
ATOM 601 CG2 THR A 3 26.807 24.118 10.507 1.00 38.32 C
TER
ATOM 70 N ALA B 2 17.139 38.489 7.542 1.00 84.40 N
ATOM 71 CA ALA B 2 16.401 39.708 7.233 1.00 82.49 C
ATOM 72 C ALA B 2 17.081 40.939 7.824 1.00 88.51 C
ATOM 73 O ALA B 2 17.221 41.955 7.138 1.00 82.84 O
ATOM 74 CB ALA B 2 14.954 39.610 7.712 1.00 80.41 C
ATOM 75 N ARG B 3 17.504 40.862 9.087 1.00 83.11 N
ATOM 76 CA ARG B 3 18.215 41.993 9.686 1.00 80.09 C
ATOM 77 C ARG B 3 19.746 41.845 9.588 1.00 86.10 C
ATOM 78 O ARG B 3 20.379 41.144 10.389 1.00 85.06 O
ATOM 79 CB ARG B 3 17.779 42.223 11.128 1.00 80.49 C
ATOM 80 CG ARG B 3 16.326 42.657 11.272 1.00 86.72 C
ATOM 81 CD ARG B 3 15.905 42.771 12.734 1.00 84.86 C
ATOM 82 NE ARG B 3 16.538 43.899 13.407 1.00 84.46 N
ATOM 83 CZ ARG B 3 16.460 44.127 14.712 1.00 85.48 C
ATOM 84 NH1 ARG B 3 15.783 43.294 15.485 1.00 84.75 N
ATOM 85 NH2 ARG B 3 17.057 45.186 15.239 1.00 89.68 N
ATOM 86 N ILE B 4 20.329 42.493 8.586 1.00 81.62 N
ATOM 87 CA ILE B 4 21.772 42.515 8.415 1.00 88.68 C
ATOM 88 C ILE B 4 22.324 43.671 9.214 1.00 84.12 C
ATOM 89 O ILE B 4 22.056 44.830 8.893 1.00 87.89 O
ATOM 90 CB ILE B 4 22.151 42.705 6.945 1.00 83.69 C
ATOM 91 CG1 ILE B 4 21.583 41.559 6.110 1.00 84.63 C
ATOM 92 CG2 ILE B 4 23.672 42.799 6.774 1.00 80.94 C
ATOM 93 CD1 ILE B 4 21.832 41.708 4.619 1.00 85.50 C
TER
ATOM 2076 N GLN C 1 -5.202 -31.148 19.518 1.00 77.90 N
ATOM 2077 CA GLN C 1 -4.657 -29.990 20.288 1.00 78.01 C
ATOM 2078 C GLN C 1 -3.890 -30.442 21.508 1.00 76.88 C
ATOM 2079 O GLN C 1 -3.784 -29.715 22.500 1.00 77.19 O
ATOM 2080 CB GLN C 1 -5.777 -29.086 20.761 1.00 79.28 C
ATOM 2081 CG GLN C 1 -5.605 -27.661 20.342 1.00 71.13 C
ATOM 2082 CD GLN C 1 -6.792 -27.230 19.563 1.00 72.49 C
ATOM 2083 OE1 GLN C 1 -7.914 -27.444 20.008 1.00 73.58 O
ATOM 2084 NE2 GLN C 1 -6.574 -26.639 18.389 1.00 73.22 N
ATOM 2085 N LYS C 2 -3.368 -31.653 21.440 1.00 75.19 N
ATOM 2086 CA LYS C 2 -2.612 -32.197 22.545 1.00 73.61 C
ATOM 2087 C LYS C 2 -1.686 -33.248 21.993 1.00 71.53 C
ATOM 2088 O LYS C 2 -2.009 -33.946 21.031 1.00 71.89 O
ATOM 2089 CB LYS C 2 -3.545 -32.831 23.588 1.00 74.00 C
ATOM 2090 CG LYS C 2 -4.381 -31.846 24.404 1.00 74.19 C
ATOM 2091 CD LYS C 2 -5.747 -32.442 24.727 1.00 75.42 C
ATOM 2092 CE LYS C 2 -6.619 -31.499 25.543 1.00 75.82 C
ATOM 2093 NZ LYS C 2 -6.281 -31.538 26.993 1.00 75.55 N
ATOM 2094 N THR C 3 -0.512 -33.331 22.592 1.00 79.45 N
ATOM 2095 CA THR C 3 0.451 -34.328 22.187 1.00 77.41 C
ATOM 2096 C THR C 3 -0.247 -35.666 22.381 1.00 76.63 C
ATOM 2097 O THR C 3 -1.086 -35.814 23.270 1.00 76.24 O
ATOM 2098 CB THR C 3 1.689 -34.276 23.070 1.00 76.49 C
ATOM 2099 OG1 THR C 3 2.475 -33.141 22.697 1.00 75.74 O
ATOM 2100 CG2 THR C 3 2.505 -35.558 22.932 1.00 75.93 C
TER
ATOM 1 P G 0 1 -0.520 0.293 -2.149 1.00 11.89 P
ATOM 2 OP1 G 0 1 -0.096 -0.880 -2.952 1.00 14.35 O
ATOM 3 OP2 G 0 1 -1.943 0.655 -2.048 1.00 12.68 O
ATOM 4 O5' G 0 1 0.012 0.179 -0.658 1.00 10.34 O
ATOM 5 C5' G 0 1 1.425 -0.140 -0.414 1.00 40.00 C
ATOM 6 C4' G 0 1 1.652 -0.059 1.077 1.00 40.00 C
ATOM 7 O4' G 0 1 1.483 1.323 1.502 1.00 40.00 O
ATOM 8 C3' G 0 1 0.670 -0.857 1.928 1.00 40.00 C
ATOM 9 O3' G 0 1 1.119 -2.195 2.125 1.00 40.00 O
ATOM 10 C2' G 0 1 0.631 -0.058 3.224 1.00 40.00 C
ATOM 11 O2' G 0 1 1.777 -0.309 4.016 1.00 40.00 O
ATOM 12 C1' G 0 1 0.707 1.369 2.686 1.00 40.00 C
ATOM 13 N9 G 0 1 -0.595 1.945 2.360 1.00 40.00 N
ATOM 14 C8 G 0 1 -0.999 2.449 1.148 1.00 40.00 C
ATOM 15 N7 G 0 1 -2.227 2.891 1.157 1.00 40.00 N
ATOM 16 C5 G 0 1 -2.660 2.667 2.458 1.00 40.00 C
ATOM 17 C6 G 0 1 -3.910 2.942 3.072 1.00 40.00 C
ATOM 18 O6 G 0 1 -4.921 3.452 2.573 1.00 40.00 O
ATOM 19 N1 G 0 1 -3.919 2.556 4.407 1.00 40.00 N
ATOM 20 C2 G 0 1 -2.864 1.980 5.067 1.00 40.00 C
ATOM 21 N2 G 0 1 -3.068 1.679 6.352 1.00 40.00 N
ATOM 22 N3 G 0 1 -1.696 1.719 4.510 1.00 40.00 N
ATOM 23 C4 G 0 1 -1.663 2.086 3.213 1.00 40.00 C
ATOM 24 P C 0 2 0.081 -3.417 1.982 1.00 70.30 P
ATOM 25 OP1 C 0 2 0.874 -4.672 1.982 1.00 70.30 O
ATOM 26 OP2 C 0 2 -0.835 -3.128 0.849 1.00 70.30 O
ATOM 27 O5' C 0 2 -0.766 -3.362 3.330 1.00 70.30 O
ATOM 28 C5' C 0 2 -0.145 -3.573 4.598 1.00 70.30 C
ATOM 29 C4' C 0 2 -1.121 -3.275 5.712 1.00 70.30 C
ATOM 30 O4' C 0 2 -1.478 -1.866 5.658 1.00 70.30 O
ATOM 31 C3' C 0 2 -2.449 -4.016 5.632 1.00 70.30 C
ATOM 32 O3' C 0 2 -2.375 -5.296 6.256 1.00 70.30 O
ATOM 33 C2' C 0 2 -3.398 -3.071 6.358 1.00 70.00 C
ATOM 34 O2' C 0 2 -3.249 -3.172 7.762 1.00 70.00 O
ATOM 35 C1' C 0 2 -2.865 -1.713 5.906 1.00 70.00 C
ATOM 36 N1 C 0 2 -3.504 -1.202 4.681 1.00 70.00 N
ATOM 37 C2 C 0 2 -4.815 -0.721 4.753 1.00 70.00 C
ATOM 38 O2 C 0 2 -5.405 -0.742 5.843 1.00 70.00 O
ATOM 39 N3 C 0 2 -5.407 -0.246 3.635 1.00 70.00 N
ATOM 40 C4 C 0 2 -4.741 -0.240 2.480 1.00 70.00 C
ATOM 41 N4 C 0 2 -5.366 0.240 1.406 1.00 70.00 N
ATOM 42 C5 C 0 2 -3.406 -0.726 2.375 1.00 70.00 C
ATOM 43 C6 C 0 2 -2.832 -1.195 3.490 1.00 70.00 C
ATOM 44 P U 0 3 -3.426 -6.445 5.852 1.00 40.00 P
ATOM 45 OP1 U 0 3 -2.981 -7.702 6.504 1.00 40.00 O
ATOM 46 OP2 U 0 3 -3.622 -6.412 4.380 1.00 40.00 O
ATOM 47 O5' U 0 3 -4.787 -5.982 6.539 1.00 40.00 O
ATOM 48 C5' U 0 3 -4.920 -5.945 7.959 1.00 40.00 C
ATOM 49 C4' U 0 3 -6.375 -5.805 8.344 1.00 40.00 C
ATOM 50 O4' U 0 3 -6.778 -4.418 8.156 1.00 40.00 O
ATOM 51 C3' U 0 3 -7.356 -6.613 7.501 1.00 40.00 C
ATOM 52 O3' U 0 3 -7.531 -7.932 8.010 1.00 40.00 O
ATOM 53 C2' U 0 3 -8.626 -5.778 7.591 1.00 40.00 C
ATOM 54 O2' U 0 3 -9.262 -5.944 8.844 1.00 40.00 O
ATOM 55 C1' U 0 3 -8.042 -4.369 7.518 1.00 40.00 C
ATOM 56 N1 U 0 3 -7.851 -3.876 6.146 1.00 40.00 N
ATOM 57 C2 U 0 3 -8.904 -3.213 5.545 1.00 40.00 C
ATOM 58 O2 U 0 3 -9.971 -3.025 6.099 1.00 40.00 O
ATOM 59 N3 U 0 3 -8.660 -2.778 4.269 1.00 40.00 N
ATOM 60 C4 U 0 3 -7.501 -2.931 3.546 1.00 40.00 C
ATOM 61 O4 U 0 3 -7.437 -2.480 2.403 1.00 40.00 O
ATOM 62 C5 U 0 3 -6.460 -3.627 4.234 1.00 40.00 C
ATOM 63 C6 U 0 3 -6.662 -4.068 5.479 1.00 40.00 C
TER
END
Example 5. Estimates of model accuracy prediction
(A)
QMODE1. Global Model Quality Score
PFRMAT QA
TARGET T0999
AUTHOR 1234-5678-9000
METHOD Description of methods used
MODEL 1
QMODE 1
T1031TS000_1o 0.8 0.4
T1031TS999_1o 0.7 X
END
(B)
QMODE2. Residue-based Interface Assessment
PFRMAT QA
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Reliability of residues being in Interfaces
METHOD Description of methods used
MODEL 1
QMODE 2
T1031TS000_1o 0.8 0.4 A1:0.9 A3:0.9 A17:0.7 A19:0.7 B45:0.7 B49:0.4
B50:0.4 B53:0.8
T1031TS999_1o 0.7 X A15:0.5 A17:0.9 A44:0.7 A46:0.7 B4:0.3 B9:0.4
END
Example 6. Ligand prediction
PFRMAT LG
TARGET T1999
AUTHOR My_group
METHOD LG prediction
METHOD -------------
MODEL 1
LIGAND 001 LIG
POSE 1
LIG
RDKit 3D
16 17 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 0
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
8 9 2 0
8 10 1 0
10 11 2 0
11 12 1 0
12 13 2 0
13 14 1 0
7 15 1 0
15 16 1 0
16 4 1 0
14 10 1 0
M END
POSE 2
LIG
RDKit 3D
16 17 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 0
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
8 9 2 0
8 10 1 0
10 11 2 0
11 12 1 0
12 13 2 0
13 14 1 0
7 15 1 0
15 16 1 0
16 4 1 0
14 10 1 0
M END
LIGAND 002 LIG
POSE 1
LIG
RDKit 3D
16 17 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 0
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
8 9 2 0
8 10 1 0
10 11 2 0
11 12 1 0
12 13 2 0
13 14 1 0
7 15 1 0
15 16 1 0
16 4 1 0
14 10 1 0
M END
LIGAND 003 MG
POSE 1
MG
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 Mg 0 0 0 0 0 15 0 0 0 0 0 0
M CHG 1 1 2
M END
END
MODEL 2
LIGAND 001 LIG
POSE 1
...
M END
POSE 2
...
M END
LIGAND 002 LIG
POSE 1
...
M END
LIGAND 003 MG
POSE 1
...
M END
END
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